From b5ee48a86e4b1d4c05aaadb80b44954e2e994ebc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 May 2020 07:12:51 +0200 Subject: Add docs generated using released version 0.9.52 --- docs/articles/web_only/NAFTA_examples.html | 175 +++++++++++++++-------------- 1 file changed, 91 insertions(+), 84 deletions(-) (limited to 'docs/articles/web_only/NAFTA_examples.html') diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 46cb7aa5..b91e7ee7 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -100,10 +97,10 @@

    Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/web_only/NAFTA_examples.rmd - + Source: vignettes/web_only/NAFTA_examples.Rmd + @@ -153,7 +150,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.17e-12 5.00e-01 0.0000 Inf +## k2 2.86e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -162,7 +159,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.83e+11 3.20e+11 +## DFOP 55.5 4.42e+11 2.42e+11 ## ## Representative half-life: ## [1] 321.51 @@ -201,7 +198,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.04e-11 5.00e-01 0.0000 Inf +## k2 1.16e-11 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -210,7 +207,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.09e+11 6.67e+10 +## DFOP 83.6 9.80e+10 5.98e+10 ## ## Representative half-life: ## [1] 215.87 @@ -249,7 +246,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.88e-11 5.00e-01 0.0000 Inf +## k2 4.90e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -258,7 +255,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 8.42e+09 1.79e+10 +## DFOP 34.1 6.66e+09 1.41e+10 ## ## Representative half-life: ## [1] 53.17 @@ -297,7 +294,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.30e-10 5.00e-01 0.0000 Inf +## k2 1.97e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -306,7 +303,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 5.95e+09 3.01e+09 +## DFOP 96.4 6.97e+09 3.52e+09 ## ## Representative half-life: ## [1] 454.55 @@ -402,7 +399,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 6.69e-13 5.00e-01 0.000 Inf +## k2 6.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -411,7 +408,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.86e+12 1.04e+12 +## DFOP 10.5 2.07e+12 1.15e+12 ## ## Representative half-life: ## [1] 101.43 @@ -421,11 +418,16 @@

    Example on page 9, lower panel

    p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
    +
    ## Warning in sqrt(diag(covar)): NaNs produced
    +
    ## Warning in sqrt(diag(covar_notrans)): NaNs produced
    +
    ## Warning in sqrt(1/diag(V)): NaNs produced
    +
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    ## The half-life obtained from the IORE model may be used
    -
    plot(p9b)
    +
    plot(p9b)

    -
    print(p9b)
    +
    print(p9b)
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 35.64867 23.22334 35.64867 
@@ -452,7 +454,7 @@
 ## parent_0  94.7123 1.61e-16 93.1355 96.2891
 ## k1         0.0389 1.43e-06  0.0312  0.0485
 ## k2         0.0389 6.67e-03  0.0186  0.0812
-## g          0.7742 5.00e-01  0.0000  1.0000
+## g          0.7742      NaN      NA      NA
 ## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
@@ -469,12 +471,12 @@
 
    
 
    
 Example on page 10
    
-
    p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
    
+
    p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p10)
    
+
    plot(p10)
    
 
    
-
    print(p10)
    
+
    print(p10)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 899.4089 336.4348 899.4089 
@@ -497,12 +499,12 @@
 ## sigma                   4.90 1.77e-04  2.837   6.968
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower   Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.810
-## k1         0.0495 6.48e-04  0.0303   0.081
-## k2         0.0495 1.67e-02  0.0201   0.122
-## g          0.6634 5.00e-01  0.0000   1.000
-## sigma      8.0152 2.50e-04  4.5886  11.442
+##          Estimate   Pr(>t)   Lower    Upper
+## parent_0 101.7315 1.41e-09 91.6534 111.8097
+## k1         0.0495 6.42e-04  0.0301   0.0814
+## k2         0.0495 1.66e-02  0.0200   0.1225
+## g          0.6634 5.00e-01  0.0000   1.0000
+## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
 ## 
 ## DTx values:
@@ -522,12 +524,12 @@
 
    
 
    
 Example on page 11
    
-
    p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
    
+
    p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p11)
    
+
    plot(p11)
    
 
    
-
    print(p11)
    
+
    print(p11)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 579.6805 204.7932 144.7783 
@@ -565,7 +567,7 @@
 ## DFOP 4.21e+11 2.64e+12 9.56e+11
 ## 
 ## Representative half-life:
-## [1] 41148171
    
+## [1] 41148169
    
 
    In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.
    
 
    
 
@@ -576,14 +578,14 @@
 
    
 
    
 Example on page 12, upper panel
    
-
    p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])
    
+
    p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])
    
 
    ## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p12a)
    
+
    plot(p12a)
    
 
    
-
    print(p12a)
    
+
    print(p12a)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 695.4440 220.0685 695.4440 
@@ -608,8 +610,8 @@
 ## $DFOP
 ##          Estimate   Pr(>t)   Lower   Upper
 ## parent_0  100.521 2.74e-10 92.2366 108.805
-## k1          0.124 5.75e-06  0.0958   0.161
-## k2          0.124 6.72e-02  0.0319   0.484
+## k1          0.124 5.74e-06  0.0958   0.161
+## k2          0.124 6.61e-02  0.0319   0.484
 ## g           0.877 5.00e-01  0.0000   1.000
 ## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
@@ -626,20 +628,20 @@
 
    
 
    
 Example on page 12, lower panel
    
-
    p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt
    
-
    ## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt
    
-
    ## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in qt(alpha/2, rdf): NaNs produced
    
+
    ## Warning in qt(1 - alpha/2, rdf): NaNs produced
    
+
    ## Warning in sqrt(diag(covar_notrans)): NaNs produced
    
+
    ## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced
    
+
    ## Warning in sqrt(1/diag(V)): NaNs produced
    
 
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p12b)
    
+
    plot(p12b)
    
 
    
-
    print(p12b)
    
+
    print(p12b)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 58.90242 19.06353 58.90242 
@@ -682,12 +684,16 @@
 
    
 
    
 Example on page 13
    
-
    p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
    
+
    p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in sqrt(1/diag(V)): NaNs produced
    
+
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p13)
    
+
    plot(p13)
    
 
    
-
    print(p13)
    
+
    print(p13)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 174.5971 142.3951 174.5971 
@@ -712,9 +718,9 @@
 ## $DFOP
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01
-## k1        0.00258 4.28e-01 1.45e-08 4.61e+02
+## k1        0.00258 4.28e-01 1.70e-08 3.92e+02
 ## k2        0.00258 3.69e-08 2.20e-03 3.03e-03
-## g         0.00442 5.00e-01 0.00e+00 1.00e+00
+## g         0.00442 5.00e-01       NA       NA
 ## sigma     3.41172 1.35e-04 2.02e+00 4.80e+00
 ## 
 ## 
@@ -731,16 +737,16 @@
 
    
 
    
 DT50 not observed in the study and DFOP problems in PestDF
    
-
    p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in sqrt(1/diag(V)): NaNs produced
    
 
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p14)
    
+
    plot(p14)
    
 
    
-
    print(p14)
    
+
    print(p14)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 48.43249 28.67746 27.26248 
@@ -766,7 +772,7 @@
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
 ## k1       9.53e-03 1.20e-01  0.00638   0.0143
-## k2       7.70e-12 5.00e-01  0.00000      Inf
+## k2       7.29e-12 5.00e-01  0.00000      Inf
 ## g        3.98e-01 2.19e-01  0.30481   0.4998
 ## sigma    1.17e+00 7.68e-06  0.77406   1.5610
 ## 
@@ -775,7 +781,7 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.48e+02 8.25e+02 2.48e+02
 ## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 2.41e+10 2.33e+11 9.00e+10
+## DFOP 2.54e+10 2.46e+11 9.51e+10
 ## 
 ## Representative half-life:
 ## [1] 6697.44
    
@@ -784,16 +790,17 @@
 
    
 
    
 N is less than 1 and DFOP fraction parameter is below zero
    
-
    p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in sqrt(diag(covar_notrans)): NaNs produced
    
+
    ## Warning in sqrt(1/diag(V)): NaNs produced
    
 
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p15a)
    
+
    plot(p15a)
    
 
    
-
    print(p15a)
    
+
    print(p15a)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 245.5248 135.0132 245.5248 
@@ -816,12 +823,12 @@
 ## sigma                  3.105 1.78e-04  1.795  4.416
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## parent_0 97.96752     NA 94.21914 101.7159
-## k1        0.00952     NA  0.00241   0.0377
-## k2        0.00952     NA  0.00747   0.0121
-## g         0.17247     NA       NA       NA
-## sigma     4.18778     NA  2.39747   5.9781
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 97.96752 2.85e-13 94.21914 101.7159
+## k1        0.00952 6.80e-02  0.00277   0.0327
+## k2        0.00952 3.82e-06  0.00902   0.0100
+## g         0.17247      NaN       NA       NA
+## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
 ## DTx values:
@@ -832,16 +839,16 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33
    
-
    p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in sqrt(1/diag(V)): NaNs produced
    
 
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p15b)
    
+
    plot(p15b)
    
 
    
-
    print(p15b)
    
+
    print(p15b)
    
 
    ## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 106.91629  68.55574 106.91629 
@@ -858,18 +865,18 @@
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower  Upper
-## parent_0               99.83 1.81e-16 97.51348 102.14
+## parent_0               99.83 1.81e-16 97.51349 102.14
 ## k__iore_parent_sink     0.38 3.22e-01  0.00352  41.05
-## N_parent                0.00 5.00e-01 -1.07696   1.08
+## N_parent                0.00 5.00e-01 -1.07695   1.08
 ## sigma                   2.21 2.57e-04  1.23245   3.19
 ## 
 ## $DFOP
 ##          Estimate Pr(>t)    Lower    Upper
-## parent_0 1.01e+02     NA 98.24464 1.04e+02
-## k1       4.86e-03     NA  0.00068 3.47e-02
-## k2       4.86e-03     NA  0.00338 6.99e-03
+## parent_0 1.01e+02     NA 9.82e+01 1.04e+02
+## k1       4.86e-03     NA 6.75e-04 3.49e-02
+## k2       4.86e-03     NA 3.37e-03 6.99e-03
 ## g        1.50e-01     NA       NA       NA
-## sigma    2.76e+00     NA  1.58208 3.94e+00
+## sigma    2.76e+00     NA 1.58e+00 3.94e+00
 ## 
 ## 
 ## DTx values:
@@ -885,14 +892,14 @@
 
    
 
    
 The DFOP fraction parameter is greater than 1
    
-
    p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])
    
+
    p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The representative half-life of the IORE model is longer than the one corresponding
    
 
    ## to the terminal degradation rate found with the DFOP model.
    
 
    ## The representative half-life obtained from the DFOP model may be used
    
-
    plot(p16)
    
+
    plot(p16)
    
 
    
-
    print(p16)
    
+
    print(p16)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3831.804 2062.008 1550.980 
@@ -917,7 +924,7 @@
 ## $DFOP
 ##          Estimate   Pr(>t)   Lower  Upper
 ## parent_0  88.5333 7.40e-18 79.9836 97.083
-## k1        18.5560 5.00e-01  0.0000    Inf
+## k1        18.5561 5.00e-01  0.0000    Inf
 ## k2         0.0776 1.41e-05  0.0518  0.116
 ## g          0.4733 1.41e-09  0.3674  0.582
 ## sigma      7.1902 2.11e-08  5.2785  9.102
-- 
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